Many regulatory steps in cellular processes, such as replication and transcription, depend upon binding of proteins to specific nucleic acid sequences. Therefore, an understanding of sequence-dependent binding dynamics in protein-nucleic acid complexes is important for gene regulation. Conventional methods for studying protein-nucleic acid interactions include DNaseI footprinting assays, electrophoretic mobility shift assays (EMSA), enzyme linked immunosorbent assays (ELISA), genetic analysis and X-ray crystallography.
EMSA, also known as gel shift assay, is used extensively in modern molecular biology for studying protein-nucleic acid interaction. This technique, however, suffers from a number of disadvantages. Firstly, use of hazardous nucleic acid probes labeled with radioactive phosphate can result in environmental and safety issues. In addition, the assay procedures are time consuming and labor-intensive. Furthermore, building of the detection facilities such as radio protection lab is subjected to stringent requirements. These disadvantages render this technique less amendable for fast and robust detection of specific protein-nucleic interactions on large scale, which are vital attributes in modern genomic research.
Chip or biosensor-based techniques, such as surface plasmon resonance (SPR) spectroscopy and transcription factor (TF) ELISA kits (Panomics Inc. Denmark), eliminate use of biohazard labels. However, these methods suffer from other limitations in association with the ‘solid-liquid phase’ binding nature, such as requirement of complex surface chemistry for probe immobilization, slow inefficient binding between probe and surface of substrate, steric effects, and tedious procedure due to the numerous rinsing steps. In addition, equipments required for detection are often expensive.
In summary, current state of the art methods are not cost effective, and are inconvenient and inefficient for large scale screening of protein-nucleic acid interaction.
It is therefore an object of the present invention to provide an alternative method which can be used for determining protein-nucleic acid interactions which overcomes at least some of the above disadvantages.